Motif Enrichment for Differentially Accessible/Binding Peaks.

Motif Enrichment for Differentially Accessible/Binding Peaks.

MotifEnrich(
  de.res,
  reg.type,
  signif = "padj",
  signif.threshold = 0.05,
  l2fc.threshold = 0,
  homer.motif.path = NULL,
  genome = "mm10",
  out.folder = NULL,
  other.paras = NULL
)

Arguments

de.res

Differential analysis results of peak-related data.
reg.type

The regulation type, choose from Up_regulated, Not_regulated, Down_regulated.
signif

Significance criterion to get differential peaks. For DESeq2 results, can be chosen from padj, pvalue. For edgeR results, can be chosen from FDR, PValue. Default: padj.
signif.threshold

Significance threshold to get differential peaks. Default: 0.05.
l2fc.threshold

Log2 fold change threshold to get differential peaks. Default: 0.
homer.motif.path

The path to Homer's findMotifsGenome.pl. Default: NULL.
genome

Parameter for findMotifsGenome.pl, can be genome FASTA files or pre-build genome info. Default: mm10.
out.folder

The output folder. Default: NULL (current directory).
other.paras

Parameter for findMotifsGenome.pl, can be '-len 8,10,12 -size -100,50 -S 25'. Default: NULL.

Value

Examples

# dds.peak.results.ordered is differential analysis of peak-related data.
# peak.motif = MotifEnrich(de.res = dds.peak.results.ordered, reg.type = "Up_regulated",
#                          homer.motif.path = '~/anaconda3/bin/findMotifsGenome.pl',
#                          out.folder = "/path/to/out/folder", other.paras = "-len 8,10,12 -size -100,50 -S 25")